Well, if it's a fanfiction where the train is alone, it could be haunted. There could be the ghosts of past students or even dark wizards who once used the train for their evil deeds. The train might also develop a consciousness and start to communicate with those who are brave enough to board it. It could lead the characters on a journey to discover secrets about the wizarding world that were long forgotten.
In a fanfiction about the Harry Potter train being alone, perhaps it could become a magical entity on its own. It might start to travel to mysterious destinations not on the regular Hogwarts route. Maybe it would pick up lost magical creatures or even lost wizards from different eras. It could be a place of refuge for those in need, with its compartments transforming into mini - magical habitats.
A 'Harry Potter train's alone' fanfiction could have a plot where the train is abducted by a powerful dark force. The train has to fight back using its own magical properties. It could call on the spirits of the railway tracks or the magic of the surrounding forests to help it. Or perhaps the train discovers that it has a long - lost sibling in the form of another magical vehicle, and it goes on a quest to find it while being alone.
Well, in such a fanfiction, perhaps the train could be a key to finding Flamel's hidden secrets. Maybe it has some sort of magic protection put in place by Flamel himself. It could be that the train is transporting something very important related to Flamel, like a special ingredient for his alchemy.
Maybe Harry has to find an alternative way to get to school. He could use magic to apparate or fly on a broomstick.
In a 'Harry missed the train' fanfiction, he might have to find an alternative way to get to Hogwarts. Maybe he'll use magic that he's not supposed to use yet, like apparating. This could lead to all sorts of adventures and getting into trouble with the Ministry of Magic.
Sasuke's alone time in fanfiction could involve him training intensively. He might be in a secluded forest, practicing his new jutsu. His Sharingan could be glowing as he focuses on perfecting his moves, lost in his own world of self - improvement.
Maybe he has to find an alternative way to get to school. He could try to use magic to create a makeshift transportation or ask for help from his friends' families who might be passing by.
Well, in this fanfiction, they might start to develop a new friendship on the train during their 3rd year. They could share secrets or talk about their hopes for the new school year. Daphne might be reading a really interesting book and Harry could ask her about it, starting a conversation that leads to them getting to know each other better.
Perhaps they exchange books right away. Harry shows Daphne his spell - books, and Daphne offers him one of her advanced potions books. This simple act of sharing could spark a connection between them. They might then sit together for the rest of the train ride, chatting about the upcoming school year and speculating on what new adventures and challenges await them at Hogwarts.
Maybe he's frustrated with all the prophecies and his role in the fight against Voldemort. He doesn't want to be constantly pushed into being the hero. He might want some time to figure out who he really is outside of all these expectations. Also, he could be feeling a bit overwhelmed with his studies and the extra - curricular activities like being in Dumbledore's Army. All these things together make him long for some solitude.
In some fanfictions, Harry Potter might discover a hidden magical object in the bathroom. For example, a secret passage could be revealed behind a mirror or a sink when he's in there alone, leading him to a new adventure or a place filled with ancient magic.